Method to predict response to pharmacological chaperone treatment of diseases

ABSTRACT

The present invention provides methods to determine whether a patient with a lysosomal storage disorder will benefit from treatment with a specific pharmacological chaperone. The present invention exemplifies an in vitro method for determining α-galactosidase A responsiveness to a pharmacological chaperone such as 1-deoxygalactonojirimycin in a cell line expressing a mutant from of α-galactosidase A. The invention also provides a method for diagnosing Fabry disease in patients suspected of having Fabry disease.

CROSS-REFERENCE TO RELATED APPLICATIONS

This present application is a divisional application of U.S. patentapplication Ser. No. 15/268,662, filed Sep. 19, 2016, which is acontinuation of U.S. patent application Ser. No. 14/731,603 filed Jun.5, 2015, now U.S. Pat. No. 9,545,397, which is a continuation of U.S.patent application Ser. No. 14/054,369, filed Oct. 15, 2013, now U.S.Pat. No. 9,905,584, which is a divisional of U.S. patent applicationSer. No. 12/855,468, filed Aug. 12, 2010, now U.S. Pat. No. 8,592,362,which is a continuation of International Application No.PCT/US09/033963, filed Feb. 12, 2009, U.S. Provisional PatentApplication No. 61/028,141 filed Feb. 12, 2008, U.S. Provisional PatentApplication No. 61/035,684, filed Mar. 11, 2008, U.S. Provisional PatentApplication No. 61/093,631, filed Sep. 2, 2008 and U.S. ProvisionalPatent Application No. 61/113,496, filed Nov. 11, 2008. Each of theseapplications are hereby incorporated by reference and their entirety.

FIELD OF THE INVENTION

The present invention provides methods to determine whether a patientwith a lysosomal storage disorder will benefit from treatment with aspecific pharmacological chaperone. The present invention also providesan in vitro method for determining enzyme (e.g., α-galactosidase A,α-glucosidase or glucocerebrosidase) responsiveness to a pharmacologicalchaperone (e.g., 1-deoxygalactonojirimycin, l-deoxynojirimycin orisofagomine) in a cell line expressing a mutant form of the enzyme. Theinvention also provides a method for diagnosing a lysosomal storagedisorder (e.g., Fabry disease, Pompe disease or Gaucher disease) inpatients suspected of having a lysosomal storage disorder, andimplementing the proper treatment based on the diagnosis (e.g., choosinga particular therapeutic agent to administer to the patient).

BACKGROUND

In the human body, proteins are involved in almost every aspect ofcellular function. Proteins are linear strings of amino acids that foldand twist into specific three-dimensional shapes in order to functionproperly. Certain human diseases result from mutations that causechanges in the amino acid sequence of a protein which reduce itsstability and may prevent it from folding properly. The majority ofgenetic mutations that lead to the production of less stable ormisfolded proteins are called missense mutations. These mutations resultin the substitution of a single amino acid for another in the protein.Because of this error, missense mutations often result in proteins thathave a reduced level of biological activity. In addition to missensemutations, there are also other types of mutations that can result inproteins with reduced biological activity.

Proteins generally fold in a specific region of the cell known as theendoplasmic reticulum, or ER. The cell has quality control mechanismsthat ensure that proteins are folded into their correctthree-dimensional shape before they can move from the ER to theappropriate destination in the cell, a process generally referred to asprotein trafficking. Misfolded proteins are often eliminated by thequality control mechanisms after initially being retained in the ER. Incertain instances, misfolded proteins can accumulate in the ER beforebeing eliminated.

The retention of misfolded proteins in the ER interrupts their propertrafficking, and the resulting reduced biological activity can lead toimpaired cellular function and ultimately to disease. In addition, theaccumulation of misfolded proteins in the ER may lead to various typesof stress on cells, which may also contribute to cellular dysfunctionand disease.

Lysosomal storage diseases (LSDs) are characterized by deficiencies oflysosomal enzymes due to mutations in the genes encoding the lysosomalenzymes. This results in the pathologic accumulation of substrates ofthose enzymes, which include lipids, carbohydrates, and polysaccharides.There are about fifty known LSDs to date, which include Gaucher disease,Fabry disease, Pompe disease, Tay Sachs disease and themucopolysaccharidoses (MPS). Most LSDs are inherited as an autosomalrecessive trait, although males with Fabry disease and MPS II arehemizygotes because the disease genes are encoded on the X chromosome.For most LSDs, there is no available treatment beyond symptomaticmanagement. For several LSDs, including Gaucher, Fabry, Pompe, and MPS Iand VI, enzyme replacement therapy (ERT) using recombinant enzymes isavailable. For Gaucher disease, substrate reduction therapy (SRT) alsois available in limited situations. SRT employs a small moleculeinhibitor of an enzyme required for the synthesis of glucosylceramide(the GD substrate). The goal of SRT is to reduce production of thesubstrate and reduce pathologic accumulation.

Although there are many different mutant genotypes associated with eachLSD, some of the mutations, including some of the most prevalentmutations, are missense mutations which can lead to the production of aless stable enzyme. These less stable enzymes are sometimes prematurelydegraded by the ER-associated degradation pathway. This results in theenzyme deficiency in the lysosome, and the pathologic accumulation ofsubstrate. Such mutant enzymes are sometimes referred to in thepertinent art as “folding mutants” or “conformational mutants.”

Diagnosis of Fabry Disease

Because Fabry disease is rare, involves multiple organs, has a wide agerange of onset, and is heterogeneous, proper diagnosis is a challenge.Awareness is low among health care professionals and misdiagnoses arefrequent. Some examples of diagnoses seriously considered in patientswho were eventually diagnosed with Fabry's disease include: mitral valveprolapse, glomerulonephritis, idiopathic proteinuria, systemic lupuserythematosus, Whipple's disease, acute abdomen, ulcerative colitis,acute intermittent porphyrias, and occult malignancies. Thus, even forclassically affected males, diagnosis typically takes from about 5-7years or even longer. This is a concern because the longer a person hasFabry disease, the more damage is likely to occur in the affected organsand tissues and the more serious the person's condition may become.Diagnosis of Fabry disease is most often confirmed on the basis ofdecreased α-Gal A activity in plasma or peripheral leukocytes (WBCs)once a patient is symptomatic, coupled with mutational analysis. Infemales, diagnosis is even more challenging since the enzymaticidentification of carrier females is less reliable due to randomX-chromosomal inactivation in some cells of carriers. For example, someobligate carriers (daughters of classically affected males) have α-Gal Aenzyme activities ranging from normal to very low activities. Sincecarriers can have normal α-Gal A enzyme activity in leukocytes, only theidentification of an α-Gal A mutation by genetic testing providesprecise carrier identification and/or diagnosis.

Treatment of Fabry Disease

One approved therapy for treating Fabry disease diseases is enzymereplacement therapy, which typically involves intravenous, infusion of apurified form of the corresponding wild-type protein (Fabrazyme®,Genzyme Corp.). One of the main complications with protein replacementtherapy is attainment and maintenance of therapeutically effectiveamounts of protein in vivo due to rapid degradation of the infusedprotein. The current approach to overcome this problem is to performnumerous costly high dose infusions.

Protein replacement therapy has several additional caveats, such asdifficulties with large-scale generation, purification, and storage ofproperly folded protein; obtaining glycosylated native protein;generation of an anti-protein immune response; and inability of proteinto cross the blood-brain barrier to mitigate central nervous systempathologies (i.e., low bioavailability). In addition, replacement enzymecannot penetrate the heart or kidney in sufficient amounts to reducesubstrate accumulation in the renal podocytes or cardiac myocytes, whichfigure prominently in Fabry pathology.

Gene therapy using recombinant vectors containing nucleic acid sequencesthat encode a functional protein, or using genetically modified humancells that express a functional protein, is also being developed totreat protein deficiencies and other disorders that benefit from proteinreplacement.

A third, relatively recent approach to treating some enzyme deficienciesinvolves the use of small molecule inhibitors to reduce production ofthe natural substrate of deficient enzyme proteins, thereby amelioratingthe pathology. This “substrate reduction” approach has been specificallydescribed for a class of about 40 related enzyme disorders calledlysosomal storage disorders that include glycosphingolipid storagedisorders. The small molecule inhibitors proposed for use as therapy arespecific for inhibiting the enzymes involved in synthesis ofglycolipids, reducing the amount of cellular glycolipid that needs to bebroken down by the deficient enzyme.

It has previously been shown that the binding of small moleculeinhibitors of enzymes associated with LSDs can increase the stability ofboth mutant enzyme and the corresponding wild-type enzyme (sec U.S. Pat.Nos. 6,274,597; 6,583,158; 6,589.964; 6,599,919; 6,916,829, and7,141,582 all incorporated herein by reference). In particular, it wasdiscovered that administration of small molecule derivatives of glucoseand galactose, which are specific, selective competitive inhibitors forseveral target lysosomal enzymes, effectively increased the stability ofthe enzymes in cells in vitro and, thus, increased trafficking of theenzymes to the lysosome. Thus, by increasing the amount of enzyme in thelysosome, hydrolysis of the enzyme substrates is expected to increase.The original theory behind this strategy was as follows: since themutant enzyme protein is unstable in the ER (Ishii et al., Biochem.Biophys. Res. Comm. 1996; 220: 812-815), the enzyme protein is retardedin the normal transport pathway (ER→Golgi apparatus→endosomes→lysosome)and prematurely degraded. Therefore, a compound which binds to andincreases the stability of a mutant enzyme, may serve as a “chaperone”for the enzyme and increase the amount that can exit the ER and move tothe lysosomes. In addition, because the folding and trafficking of somewild-type proteins is incomplete, with up to 70% of some wild-typeproteins being degraded in some instances prior to reaching their finalcellular location, the chaperones can be used to stabilize wild-typeenzymes and increase the amount of enzyme which can exit the ER and betrafficked to lysosomes. This strategy has been shown to increaseseveral lysosomal enzymes in vitro and in vivo, includingβ-glucocerebrosidase and α-glucosidase, deficiencies of which areassociated with Gaucher and Pompe disease, respectively.

However, as indicated above, successful candidates for SPC therapyshould have a mutation which results in the production of an enzyme thathas the potential to be stabilized and folded into a conformation thatpermits trafficking out of the ER. Mutations which severely truncate theenzyme, such as nonsense mutations, or mutations in the catalytic domainwhich prevent binding of the chaperone, will not be as likely to be“rescuable” or “enhanceable” using SPC therapy, i.e., to respond to SPCtherapy. While missense mutations outside the catalytic site are morelikely to be rescuable using SPCs, there is no guarantee, necessitatingscreening for responsive mutations. This means that, even when Fabrydisease is diagnosed by detecting deficient α-Gal A activity in WBCs, itis very difficult, if not impossible, to predict whether a particularFabry patient will respond to treatment with an SPC without benefit ofthe present invention. Moreover, since WBCs only survive for a shortperiod of time in culture (in vitro), screening for SPC enhancement ofα-Gal A is difficult and not optimal for the patient.

In order to apply SPC therapy effectively, a broadly applicable, fastand efficient method for screening patients for responsiveness to SPCtherapy needs to be adopted prior to initiation of treatment. Treatmentcan then be implemented based on the results of the screening. Thus,there remains in the art a need for relatively non-invasive methods torapidly assess enzyme enhancement with potential therapies prior tomaking treatment decisions, for both cost and emotional benefits to thepatient.

SUMMARY OF THE INVENTION

One embodiment of the present invention provides a method fordetermining whether a patient will be a candidate for SPC therapy.Specifically, the present invention provides an in vitro assay toevaluate protein activity in the presence or absence of an SPC, whereinan SPC that increases the activity of the protein in the in vitro assayis an SPC that can be used for SPC therapy. In one embodiment, the invitro assay comprises expressing a mutant protein in a host cell,contacting the mutant protein with a candidate SPC, and determining ifthe mutant protein contacted with the SPC exhibits an increased level ofactivity (preferably a statistically significant increase) when comparedto a mutant protein expressed in a host cell that is not contacted withthe candidate SPC. When a candidate SPC increases the activity of amutant protein according to the assay of the invention, such a candidateSPC can be used for SPC therapy to treat a patient expressing the samemutant protein tested in the in vitro assay.

In one embodiment, the protein is an enzyme. In another embodiment, theprotein is a lysosomal enzyme. In yet another embodiment, the protein isα-galactosidase A (α-GAL; α-GAL A). In other embodiments, the protein isalpha-glucosidase (Acid α-glucosidase; α-glucosidase; GAA). In otherembodiments, the protein is glucocerebrosidase (β-glucosidase; Gba;GCase).

The present invention also includes the basis for evaluation of SPC as atreatment option for any number of other protein abnormalities and/orenzyme deficiencies and/or a protein folding disorders.

The present invention further provides a written record (e.g., a“treatment reference table”) listing protein mutations and theresponsiveness of each of the mutations to SPC therapy. Such a list canbe used in determining treatment options for a patient, whereby thepatient, or the patient's physician or doctor, can select the propertherapeutic approach, for example, an SPC for treatment by identifyingthe patient's protein mutation, and cross-referencing the mutation withthe list to identify whether an SPC will increase the activity of thepatients particular mutant enzyme.

In another embodiment, the “treatment reference table” lists mutationsfor a lysosomal enzyme, and the treatment reference table is employed todetermine the best therapeutic approach to treat a lysosomal storagedisorder. In a further embodiment of the invention, the protein is α-GalA, and the disease is Fabry disease. In other embodiments of theinvention, the protein is GAA, and the disease is Pompe disease. Inother embodiments of the invention, the protein is Gba, and the diseaseis Gaucher disease.

In one embodiment, the treatment reference table describes mutant formsof enzyme, such as a lysomal enzyme (e.g., α-Gal A, Gcase, and GAA) andtreatment options are ascertained for lysosomal storage disorders (e.g.,Fabry, Gacher and Pompe Disease).

In one embodiment, the invention also provides for methods of creating atreatment reference table, wherein the treatment reference table can befor any protein folding disorder or disorder treatable with an SPC. Thisclass of disease includes the other lysosomal storage disorders, CysticFibrosis (CFTR) (respiratory or sweat gland epithelial cells), familialhypercholesterolemia (LDL receptor; LPL-adipocytes or vascularendothelial cells), cancer (p53; PTEN-tumor cells), and amyloidoses(transthyretin) among others.

In another embodiment, the present invention provides for methods oftreating a patient diagnosed as expressing certain mutant proteins(e.g., lysosomal enzymes such as α-GAL A), wherein activity of themutant protein (e.g., α-Gal A), when expressed in a host cell, can beincreased upon administration of an SPC for that protein (for example,1-deoxygalactonojirimycin, DGJ, as an SPC for mutant α-GAL A).

The present invention also provides for diagnostic kits containing thecomponents required to perform the assay.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1A-C. Shows a listing of Fabry mutations generated by site-directedmutagenesis. The text indicates whether HEK-293 cells expressing each ofthe listed mutations responds to DGJ treatment in the transienttransfection assay: italics=not yet tested; bold and underscored=noresponse to DGJ; plain text (not italicized, bold, orunderscored)=response to DGJ.

FIG. 2A-C Shows the responsiveness of different α-Gal A mutations to DGJtreatment. The magnitude of increase in α-Gal A activity levels afterDGJ treatment and EC50 values are listed for every tested mutation inFIG. 1A-D that responded to DGJ treatment. The increase in enzymeactivity is shown as a percentage of wild type α-Gal A activity.

FIG. 3 Shows representative examples of wild type and mutant α-Gal Aresponses to DGJ treatment. α-Gal A activity (expressed as nmol/mgprotein/hr of 4-MU released) was measured in lysates prepared fromtransfected HEK 293 cells incubated with increasing concentrations ofDGJ. A typical concentration-dependent response is shown for L300P and atypical negative response to DGJ is shown for R227Q. Wild type exhibitshigh baseline activity and thus does not respond to DGJ in this assay.

FIG. 4 Shows that the mutation response in HEK 293 cells are comparableto patient-derived T-cells, lymphoblasts or white blood cells in vivo.α-Gal A levels measured in three different assays, reported aspercentage of wild type, are compared for each mutation examined, α-GalA levels were measured in T-Cells, lymphoblasts, white blood cells andHEK 293 cells expressing mutant α-Gal A before and after exposure toDGJ. Blank bars indicate basal level (without DGJ treatment) and filledbars indicate the elevated level after DGJ treatment.

FIG. 5 Shows that DGJ-responsive α-Gal A mutations are widelydistributed on the α-Gal A protein sequence. Tested Fabry mutations areillustrated on the α-Gal A secondary structure. No significantcorrelation between response and location on the protein sequence of amutation was observed, suggesting that responsive as well asnon-responsive mutations are distributed widely across the entireprotein. Text color indicates DGJ response: green=response; red=noresponse; brown indicates that of the multiple mutations on that samesite some responded to DGJ treatment, while others did not.

FIG. 6 Shows the oligonucleotide primer pairs used to generate the pointmutations in the α-Gal A gene through site-directed mutagenesis.

FIG. 7 Shows the α-Gal A eDNA sequence that was mutated through thesite-directed mutagenesis.

FIG. 8 Shows the effect of isofagomine tartrate on patient-derivedmacrophages and lymphoblasts isolated from Gaucher disease patients withdifferent mutations in their glucocerebrosidase (Gba; GCase) enzyme.

FIG. 9 Shows the effect on GL-3 levels of eight-week old male hR301Qα-Gal A Tg/KO mice which were treated for 4 weeks with 300 mg/kg DGJ indrinking water either daily or less frequently (4 days ON/3 days OFF).

FIG. 10 Shows a listing of Pompe mutations generated by site-directedmutagenesis. The text indicates whether COS-7 cells expressing each ofthe listed mutations responds to DNJ treatment in the transienttransfection assay.

FIGS. 11A and 11B Show the nucleic acid sequence of human lysosomalalpha-glucosidase (GAA) (GenBank Accession No.: Y00839).

FIG. 12 Shows the responsiveness of four different GAA mutations to DNJtreatment at concentrations of 0 μM, 20 μM, 50 μM and 100 μM. Theincrease in enzyme activity is shown as specific activity (nmol/mgprotein/hour). FIG. 12 also shows that DNJ promoted processing of GAA tothe 95/76/70 kDa forms.

FIG. 13 Shows the responsiveness of Pompe patient-derived fibroblasts toDNJ treatment. The fibroblasts were homozygous for either the P545L orR854X GAA mutation.

FIG. 14 Shows the EC₅₀ for DNJ induced GAA activity in HEK-293 cellstransiently transfected with the P545L GAA mutation.

FIG. 15 Shows the responsiveness of Pompe patient-derived lymphocytes toDNJ treatment. The lymphocytes were heterozygous for the (IVS1AS, T>G,−13) GAA splicing defect and a GAA frameshift mutation.

FIGS. 16A, 16B, and 16C Show the amino acid sequence encoded by a humanlysosomal alpha-glucosidase (GAA) nucleic acid (GenBank Accession No.:Y00839).

DETAILED DESCRIPTION

The present invention provides an in vitro assay to provide accuratedetermination of whether an SPC enhances activity of a mutant protein.

In one embodiment, the protein is a lysosomal enzyme, wherein thelysosomal enzyme, when mutated, causes a lysosomal storage disorder. Theconcepts of the present invention, however, can be globally applied toany disease or condition characterized by mutant proteins amenable toSPC-therapy, in which the proteins have one or more specific mutationsthat can be generated in vitro, for example, by site-directedmutagenesis.

In one specific embodiment, the invention provides methods fordetermining whether an SPC enhances enzyme activity of a mutant α-Gal Aenzyme, and can therefore be utilized as an effective therapeutictreatment for a Fabry disease patient expressing the same α-Gal Amutation.

In another specific embodiment, the invention provides methods fordetermining whether an SPC enhances enzyme activity of a mutant GAAenzyme, and can therefore be utilized as an effective therapeutictreatment for a Pompe disease patient expressing the same GAA mutation.

In another specific embodiment, the invention provides methods fordetermining whether an SPC enhances enzyme activity of a mutant Gbaenzyme, and can therefore be utilized as an effective therapeutictreatment for a Gaucher disease patient expressing the same Gbamutation.

According to the methods of the present invention, assays are providedthat allow for the determination of whether a patient expressing amutant lysosomal enzyme will be a candidate for SPC therapy. The new invitro assay is extremely sensitive and can be performed on a host celltransfected with a nucleic acid construct encoding a mutant lysosomalenzyme. Specific candidate SPCs can then be assayed to determine if thecandidate SPC is capable of increasing the activity of the mutant enzymeexpressed by the host cell. Thus, unlike assays which utilize cellsderived from a patient with a lysosomal storage disorder, the assay ofthe invention avoids time consuming steps such as collection of a samplefrom a patient, purification of cells from the sample, and culturing thecells from the sample in vitro.

The present invention also provides for a method of determining whethera patient expressing a mutant protein (e.g. a lysosomal enzyme) will bea candidate for SPC therapy, wherein a person, for example, a patient'sphysician or doctor, can look up the mutant protein (e.g. a lysosomalenzyme mutation) in a treatment reference table to determine if thepatient's mutation will respond to SPC therapy. The reference table isgenerated from the results of in vitro analysis of SPC response in acell line that has been transformed with a nucleic acid vector whichencodes the mutant protein.

Furthermore, the invention also provides a “Treatment Reference Table”that provides information describing if a particular SPC will be asuccessful therapy for enhancing the activity of a specific lysosomalenzyme mutation. According to the present invention, the treatmentreference table provides information indicating if a candidate SPC canincrease the activity of a mutant lysosomal enzyme expressed by a hostcell. Based on the response of different mutations to different SPCtherapies, the present invention can provide SPC therapy tailored to thepatient's specific mutation.

In one non-limiting embodiment, the mutant protein is a mutant lysosomalenzyme, such as, for example, a mutant α-Gal A, GAA or Gba, and the cellline is transfected with a nucleic acid vector which encodes the mutantlysosomal enzyme.

In another non-limiting embodiment, the present invention provides amethod of treating a Fabry patient that includes the step ofadministering to the Fabry patient a therapeutically effective dose of1-deoxygalactonojirimycin (DGJ), wherein the patient expresses a mutantα-Gal A, the activity of which, when expressed in a host cell, can beincreased when contacted with an SPC (e.g. DGJ). Such α-Gal A mutationstreatable according to this method include, but are not limited toA121T, A156V, A20P, A288D, A288P, A292P, A348P, A73V, C52R, C94Y, D234E,D244H, D244N, D264Y, E338K, E341D, E358K, E398K, E48K, E59K, E66Q,F113L, G144V, G183D, G260A, G271S, G325D, G328A, G35R, G373D, G373S,H225R, I219N, I242N, I270T, I289F, I303N, I317T, I354K, I91T, L14P,L166V, L243F, L300F, L310F, L32P, L45R, M267I, M284T, M296I, M296V,M72V, M76R, N224S, N263S, N298K, N298S, N320I, N320Y, N34K, P205R,P259L, P265L, P265R, P293A, P293S, P409S, P40L, P40S, Q279E, Q279H,Q279R, Q280H, Q280K, Q312H, Q321E, Q321R, Q327E, R301P, R342Q, R363C,R363H, R49G, R49L, R49S, S201 Y, S276N, S297C, S345P, T194I, V269M,V316E, W340R, W47L, and W95S mutations.

In one embodiment, the following α-Gal A mutations are excluded from themethods of treating a Fabry patient with a therapeutically effectivedose of DGJ: D244N, E358K, E59K, E66Q, G183D, G325D, I289F, I91T, L45R,M296V, N263S, N320Y, P205R, P40S. Q279E, R342Q, R363C, R49L, V316E.

One advantage of the assay described by the present invention is itsapplicability to female patients with an X-linked lysosomal storagedisorder, such as Fabry disease. Because of X-chromosome inactivation, asample taken from a female patient will comprise both normal healthycells and enzyme deficient mutant cells. An assay for an SPC's effect onsuch a sample will show an enhancement in enzyme activity due to thenormal wild type enzyme expression of the healthy cells even though thediseased cells with the mutant enzyme may not be responsive to the SPC.The present invention overcomes this obstacle because a cell linetransfected with a vector encoding a mutant protein will only expressthe mutant form of the protein, and thus, there will be no wild typeprotein expressed by the cell line to cause such pseudo enhancementobserved in assays with patient derived cells.

In another non-limiting embodiment, the present invention provides amethod of treating a Pompe patient that includes the step ofadministering to the Pompe patient a therapeutically effective dose of1-deoxynojirimycin (DNJ), wherein the patient expresses a mutant GAA,the activity of which, when expressed in a host cell, can be increasedwhen contacted with an SPC (e.g. DNJ). Such GAA mutations treatableaccording to this method include, but are not limited to, E262K, P266S,P285R, P285S, L291F, L291H, L291P, M318K, G377R, A445P, Y455C, Y455F,P457L, G483R, G483V, M519V, S529V, P545L, G549R, L552P, Y575S, E579K,A610V, H612Q, A644P, and .DELTA.N470 mutations.

In another non-limiting embodiment, the present invention provides amethod of treating a Gaucher patient with a therapeutically effectivedose of isofagomine (IFG), wherein the patient expresses a mutant Gba,the activity of which, when expressed in a host cell, can be increasedwhen contacted with an SPC (e.g. IFG).

Definitions

The terms used in this specification generally have their ordinarymeanings in the art, within the context of this invention and in thespecific context where each term is used. Certain terms are discussedbelow, or elsewhere in the specification, to provide additional guidanceto the practitioner in describing the compositions and methods of theinvention and how to make and use them.

The term “Fabry disease” refers to an X-linked inborn error ofglycosphingolipid catabolism due to deficient lysosomal α-galactosidaseA activity. This defect causes accumulation of globotriaosylceramide(ceramide trihexoside) and related glycosphingolipids in vascularendothelial lysosomes of the heart, kidneys, skin, and other tissues.

The term “atypical Fabry disease” refers to patients with primarilycardiac manifestations of the α-Gal A deficiency, namely progressiveglobotriaosylceramide (GL-3) accumulation in myocardial cells that leadsto significant enlargement of the heart, particularly the leftventricle.

A “carrier” is a female who has one X chromosome with a defective α-GalA gene and one X chromosome with the normal gene and in whom Xchromosome inactivation of the normal allele is present in one or morecell types. A carrier is often diagnosed with Fabry disease.

“Pompe disease” refers to an autosomal recessive LSD characterized bydeficient acid alpha glucosidase (GAA) activity which impairs lysosomalglycogen metabolism. The enzyme deficiency leads to lysosomal glycogenaccumulation and results in progressive skeletal muscle weakness,reduced cardiac function, respiratory insufficiency, and/or CNSimpairment at late stages of disease. Genetic mutations in the GAA generesult in either lower expression or produce mutant forms of the enzymewith altered stability, and/or biological activity ultimately leading todisease. (see generally Hirschhorn R, 1995, Glycogen Storage DiseaseType 11: Acid α-Glucosidase (Acid Maltase) Deficiency, The Metabolic andMolecular Bases of Inherited Disease, Scriver et al., eds., McGraw-Hill,New York, 7th ed., pages 2443-2464). The three recognized clinical formsof Pompe disease (infantile, juvenile and adult) are correlated with thelevel of residual α-glucosidase activity (Reuser A J et al., 1995,Glycogenosis Type II (Acid Maltase Deficiency), Muscle & NerveSupplement 3, S61-S69). ASSC (also referred to elsewhere as“pharmacological chaperones”) represent a promising new therapeuticapproach for the treatment of genetic diseases, such as lysosomalstorage disorders (e.g. Pompe Disease).

Infantile Pompe disease (type I or A) is most common and most severe,characterized by failure to thrive, generalized hypotonia, cardiachypertrophy, and cardiorespiratory failure within the second year oflife. Juvenile Pompe disease (type II or B) is intermediate in severityand is characterized by a predominance of muscular symptoms withoutcardiomegaly. Juvenile Pompe individuals usually die before reaching 20years of age due to respiratory failure. Adult Pompe disease (type IIIor C) often presents as a slowly progressive myopathy in the teenageyears or as late as the sixth decade (Felice K J et al., 1995, ClinicalVariability in Adult-Onset Acid Maltase Deficiency: Report of AffectedSibs and Review of the Literature, Medicine 74, 131-135).

In Pompe, it has been shown that α-glucosidase is extensively modifiedpost-translationally by glycosylation, phosphorylation, and proteolyticprocessing. Conversion of the 110 kilodalton (kDa) precursor to 76 and70 kDa mature forms by proteolysis in the lysosome is required foroptimum glycogen catalysis.

As used herein, the term “Pompe Disease” refers to all types of PompeDisease. The formulations and dosing regimens disclosed in thisapplication may be used to treat, for example, Type I, Type II or TypeIII Pompe Disease.

The term “Gaucher disease” refers to a deficiency of the lysosomalenzyme (I-glucocerebrosidase (Gba) that breaks down fattyglucocerebrosides. The fat then accumulates, mostly in the liver, spleenand bone marrow. Gaucher disease can result in pain, fatigue, jaundice,bone damage, anemia and even death. There are three clinical phenotypesof Gaucher disease. Patients with, Type I manifest either early in lifeor in young adulthood, bruise easily and experience fatigue due toanemia, low blood platelets, enlargement of the liver and spleen,weakening of the skeleton, and in some instances have lung and kidneyimpairment. There are no signs of brain involvement. In Type II,early-onset, liver and spleen enlargement occurs by 3 months of age andthere is extensive brain involvement. There is a high mortality rate byage 2. Type III is characterized by liver and spleen enlargement andbrain seizures. The β-glucocerebrosidase gene is located on the human1q21 chromosome. Its protein precursor contains 536 amino acids and itsmature protein is 497 amino acids long.

A “patient” refers to a subject who has been diagnosed with or issuspected of having a particular disease. The patient may be human oranimal.

A “Fabry disease patient” refers to an individual who has been diagnosedwith or suspected of having Fabry disease and has a mutated α-Gal A asdefined further below. Characteristic markers of Fabry disease can occurin male hemizygotes and female carriers with the same prevalence,although females typically are less severely affected.

A “Pompe disease patient” refers to an individual who has been diagnosedwith or suspected of having Pompe disease and has a mutated GAA asdefined further below.

A “Gaucher disease patient” refers to an individual who has beendiagnosed with or suspected of having Gaucher disease and has a mutatedGba as defined further below.

Human α-galactosidase A (α-Gal A) refers to an enzyme encoded by thehuman GLA gene. The human α-Gal A enzyme consists of 429 amino acids andis in GenBank Accession No. U78027.

In one non-limiting embodiment, human lysosomal alpha-glucosidase (Acidα-glucosidase; GAA) is a lysosomal enzyme which hydrolyzes alpha-1,4-and alpha-1,6-linked-D-glucose polymers present in glycogen, maltose,and isomaltose. Alternative names are as follows: glucoamylase;1,4-α-D-glucan glucohydrolase; amyloglucosidase; gamma-amylase; andexo-1,4-α-glucosidase. The human GAA gene has been mapped to chromosome17q25.2-25.3 and has nucleotide and amino acid sequences depicted inGenBank Accession No. Y00839.

The term “human Gba gene” refers to the gene encoding acidβ-glucosidase, also referred to as glucocerebrosidase or Gba. The Gbagene is on chromosome 1q21 and involves 11 exons (GenBank Accession No.J03059). There is also a homologous pseudogene for Gba located about 16kb downstream of the Gba gene (GenBank Accession No. M16328).

The “human Gba” protein refers to the wild-type human Gba protein. TheGba protein consists of 536 amino acids and is in GenBank Accession No.J03059.

The term “mutant protein” includes a protein which has a mutation in thegene encoding the protein which results in the inability of the proteinto achieve a stable conformation under the conditions normally presentin the ER. The failure to achieve a stable conformation results in asubstantial amount of the enzyme being degraded, rather than beingtransported to the lysosome. Such a mutation is sometimes called a“conformational mutant.” Such mutations include, but are not limited to,missense mutations, and in-frame small deletions and insertions.

As used herein in one embodiment, the term “mutant α-Gal A” includes anα-Gal A which has a mutation in the gene encoding α-Gal A which resultsin the inability of the enzyme to achieve a stable conformation underthe conditions normally present in the ER. The failure to achieve astable conformation results in a substantial amount of the enzyme beingdegraded, rather than being transported to the lysosome.

Non-limiting, exemplary α-Gal A mutations associated with Fabry diseasewhich result in unstable α-Gal A include L32P; N34S; T411; M51K; E59K;E66Q; 191T; A97V; R100K; R112C; R112H; F113L; T141L; A143T; G144V;S148N; A156V; L166V; D170V; C172Y; G183D; P205T; Y207C; Y207S; N215S;A228P; S235C; D244N; P259R; N263S; N264A; G272S; S276G; Q279E; Q279K;Q279H; M284T; W287C; 1289F; M2961; M296V; L300P; R301Q; V316E; N320Y;G325D; G328A; R342Q; E358A; E358K; R363C; R363H; G370S; and P409A.

As used herein in one embodiment, the term “mutant GAA” includes a GAAwhich has a mutation in the gene encoding GAA which results in theinability of the enzyme to achieve a stable conformation under theconditions normally present in the ER. The failure to achieve a stableconformation results in a substantial amount of the enzyme beingdegraded, rather than being transported to the lysosome.

As used herein in one embodiment, the term “mutant Gba” includes a Gbawhich has a mutation in the gene encoding Gba which results in theinability of the enzyme to achieve a stable conformation under theconditions normally present in the ER. The failure to achieve a stableconformation results in a substantial amount of the enzyme beingdegraded, rather than being transported to the lysosome.

As used herein, the term “specific pharmacological chaperone” (“SPC”) or“pharmacological chaperone” refers to any molecule including a smallmolecule, protein, peptide, nucleic acid, carbohydrate, etc. thatspecifically binds to a protein and has one or more of the followingeffects: (i) enhances the formation of a stable molecular conformationof the protein; (ii) induces trafficking of the protein from the ER toanother cellular location, preferably a native cellular location, i.e.,prevents ER-associated degradation of the protein; (iii) preventsaggregation of misfolded proteins; and/or (iv) restores or enhances atleast partial wild-type function and/or activity to the protein. Acompound that specifically binds to e.g., α-Gal A, GAA or Gba, meansthat it binds to and exerts a chaperone effect on the enzyme and not ageneric group of related or unrelated enzymes. More specifically, thisterm does not refer to endogenous chaperones, such as BiP, or tonon-specific agents which have demonstrated non-specific chaperoneactivity against various proteins, such as glycerol, DMSO or deuteratedwater, i.e., chemical chaperones (see Welch et al., Cell Stress andChaperones 1996; 1(2): 109-115; Welch et al., Journal of Bioenergeticsand Biomembranes 1997; 29(5):491-502; U.S. Pat. Nos. 5,900,360;6,270,954; and 6,541,195). In the present invention, the SPC may be areversible competitive inhibitor.

A “competitive inhibitor” of an enzyme can refer to a compound whichstructurally resembles the chemical structure and molecular geometry ofthe enzyme substrate to bind the enzyme in approximately the samelocation as the substrate. Thus, the inhibitor competes for the sameactive site as the substrate molecule, thus increasing the Km.Competitive inhibition is usually reversible if sufficient substratemolecules are available to displace the inhibitor, i.e., competitiveinhibitors can bind reversibly. Therefore, the amount of enzymeinhibition depends upon the inhibitor concentration, substrateconcentration, and the relative affinities of the inhibitor andsubstrate for the active site.

Following is a description of some specific pharmacological chaperones(SPCs) contemplated by this invention:

In one particular non-limiting embodiment, the SPC isI-deoxygalactonorjirimycin which refers to a compound having thefollowing structures:

or a pharmaceutically acceptable salt, ester or prodrug of1-deoxygalactonorjirimycin. The hydrochloride salt of DGJ is known asmigalastat hydrochloride (Migalastat).

Still other SPCs for α-Gal A are described in U.S. Pat. Nos. 6,274,597,6,774,135, and 6,599,919 to Fan ct al., and includeα-3,4-di-epi-homonojirimycin, 4-epi-fagomine, α-allo-homonojirimycin,N-methyl-deoxygalactonojirimycin, β-1-C-butyl-deoxygalactonojirimycin,α-galacto-homonojirimycin, calystegine A₃, calystegine B₂, calystegineB₃, N-methyl-calystegine A₃, N-methyl-calystegine B₂ andN-methyl-calystegine B₃.

In one particular non-limiting embodiment, the SPC is isofagominc (IFG;(3R,4R,5R)-5-(hydroxymethyl)-3,4-piperidinediol) which is represented bythe following formula:

or a pharmaceutically acceptable salt, ester or prodrug of isofagomine,such as, for example, IFG tartrate (see, e.g., U.S. Patent ApplicationPublication 20070281975.) IFG has a molecular formula of C₆H₁₃NO3 and amolecular weight of 147.17. This compound is further described in U.S.Pat. No. 5,844,102 to Sierks et al., and U.S. Pat. No. 5,863,903, toLundgren et al.

Still other SPCs for Gba are described in U.S. Pat. No. 6,916,829 to Fanet al., and include C-benzyl isofagominc and derivatives, N-alkyl(C9-12)-DNJ, Glucoimidazole (and derivatives), C-alkyl-IFG (andderivatives), N-alkyl-β-valeinamines, Fluphenozine, N-dodecyl-DNJ,calystegines A₃, B₁, B₂ and C₁

In one particular non-limiting embodiment, the SPC is1-deoxynorjirimycin (1-DNJ), which is represented by the followingformula:

or a pharmaceutically acceptable salt, ester or prodrug of1-deoxynorjirimycin. In one embodiment, the salt is hydrochloride salt(i.e. 1-deoxynojirimycin-HCl).

Still other SPCs for GAA are described in U.S. Pat. Nos. 6,274,597;6,583,158; 6,599,919 and 6,916,829 to Fan et al., and U.S. PublishedApplication No. 2006/0264467, and include N-methyl-DNJ, N-ethyl-DNJ,N-propyl-DNJ, N-butyl-DNJ, N-pentyl-DNJ, N-hexyl-DNJ, N-heptyl-DNJ,N-octyl-DNJ, N-nonyl-DNJ, N-methylcyclopropyl-DNJ,N-methylcyclopentyl-DNJ, N-2-hydroxyethyl-DNJ, 5-N-carboxypentyl DNJ,α-homonojirimycin, and castanospermine.

As used herein, the term “specifically binds” refers to the interactionof a pharmacological chaperone with a protein such as α-Gal A, Gba orGAA, specifically, an interaction with amino acid residues of theprotein that directly participate in contacting the pharmacologicalchaperone. A pharmacological chaperone specifically binds a targetprotein, e.g., α-Gal A, Gba or GAA, to exert a chaperone effect on theprotein and not a generic group of related or unrelated proteins. Theamino acid residues of a protein that interact with any givenpharmacological chaperone may or may not be within the protein's “activesite.” Specific binding can be evaluated through routine binding assaysor through structural studies, e.g., co-crystallization, NMR, and thelike. The active site for α-Gal A, Gba or GAA is the substrate bindingsite.

“Deficient α-Gal A activity” refers to α-Gal A activity in cells from apatient which is below the normal range as compared (using the samemethods) to the activity in normal individuals not having or suspectedof having Fabry or any other disease (especially a blood disease).

“Deficient Gba activity” refers to Gba activity in cells from a patientwhich is below the normal range as compared (using the same methods) tothe activity in normal individuals not having or suspected of havingGaucher or any other disease.

“Deficient GAA activity” refers to GAA activity in cells from a patientwhich is below the normal range as compared (using the same methods) tothe activity in normal individuals not having or suspected of havingPompe or any other disease.

As used herein, the terms “enhance α-Gal A activity,” “enhance Gbaactivity,” and “enhance GAA activity” or “increase α-Gal A activity,”“increase Gba activity,” and “increase GAA activity” refer to increasingthe amount of α-Gal A, Gba or GAA, respectively, that adopts a stableconformation in a cell contacted with a pharmacological chaperonespecific for the α-Gal A, Gba or GAA, relative to the amount in a cell(preferably of the same cell-type or the same cell, e.g., at an earliertime) not contacted with the pharmacological chaperone specific for theα-Gal A, Gba or GAA. This term also refers to increasing the traffickingof α-Gal A, Gba or GAA to the lysosome in a cell contacted with apharmacological chaperone specific for the α-Gal A, Gba or GAA, relativeto the trafficking of α-Gal A, Gba or GAA not contacted with thepharmacological chaperone specific for the protein. These terms refer toboth wild-type and mutant α-Gal A, Gba or GAA. In one embodiment, theincrease in the amount of α-Gal A, Gba or GAA in the cell is measured bymeasuring the hydrolysis of an artificial substrate in lysates fromcells that have been treated with the SPC. An increase in hydrolysis isindicative of increased α-Gal A, Gba or GAA activity.

The term “α-Gal A activity” refers to the normal physiological functionof a wild-type α-Gal A in a cell. For example, α-Gal A activity includeshydrolysis of GL-3.

The term “Gba activity” refers to the normal physiological function of awild-type αGba in a cell. For example, Gba activity includes metabolismof fatty glucocerebrosides.

The term “GAA activity” refers to the normal physiological function of awild-type Gaa in a cell. For example, GAA activity includes lysosomalglycogen metabolism.

A “responder” is an individual diagnosed with or suspected of having alysosomal storage disorder, such, for example, but not limited to, Fabrydisease, Pompe disease or Gaucher disease, whose cells exhibitsufficiently increased α-Gal A, GAA or Gba activity, respectively,and/or amelioration of symptoms or improvement in surrogate markers, inresponse to contact with an SPC. Non-limiting examples of improvementsin surrogate markers for Fabry and Pompe disease are disclosed in U.S.Ser. Nos. 60/909,185 and 61/035,869, respectively.

Non-limiting examples of improvements in surrogate markers for Fabrydisease disclosed in U.S. Ser. No. 60/909,185 include increases in α-GalA levels or activity in cells (e.g., fibroblasts) and tissue; reductionsin of GL-3 accumulation; decreased plasma concentrations of homocysteineand vascular cell adhesion molecule-1 (VCAM-1); decreased GL-3accumulation within myocardial cells and valvular fibrocytes; reductionin cardiac hypertrophy (especially of the left ventricle), ameliorationof valvular insufficiency, and arrhythmias; amelioration of proteinuria;decreased urinary concentrations of lipids such as CTH,lactosylceramide, ceramide, and increased urinary concentrations ofglucosylceramide and sphingomyelin (Fuller et al., Clinical Chemistry.2005; 51: 688-694); the absence of laminated inclusion bodies (Zebrabodies) in glomerular epithelial cells; improvements in renal function;mitigation of hypohidrosis; the absence of angiokeratomas; andimprovements hearing abnormalities such as high frequency sensorineuralhearing loss progressive hearing loss, sudden deafness, or tinnitus.Improvements in neurological symptoms include prevention of transientischemic attack (TIA) or stroke; and amelioration of neuropathic painmanifesting itself as acroparaesthesia (burning or tingling inextremities).

The dose that achieves one or more of the aforementioned responses is a“therapeutically effective dose.”

The phrase “pharmaceutically acceptable” refers to molecular entitiesand compositions that are physiologically tolerable and do not typicallyproduce untoward reactions when administered to a human. Preferably, asused herein, the term “pharmaceutically acceptable” means approved by aregulatory agency of the Federal or a state government or listed in theU.S. Pharmacopoeia or other generally recognized pharmacopoeia for usein animals, and more particularly in humans. The term “carrier” refersto a diluent, adjuvant, excipient, or vehicle with which the compound isadministered. Such pharmaceutical carriers can be sterile liquids, suchas water and oils. Water or aqueous solution saline solutions andaqueous dextrose and glycerol solutions are preferably employed ascarriers, particularly for injectable solutions. Suitable pharmaceuticalcarriers are described in “Remington's Pharmaceutical Sciences” by E. W.Martin, 18th Edition, or other editions.

As used herein, the term “isolated” means that the referenced materialis removed from the environment in which it is normally found. Thus, anisolated biological material can be free of cellular components, i.e.,components of the cells in which the material is found or produced. Inthe case of nucleic acid molecules, an isolated nucleic acid includes aPCR product, an mRNA band on a gel, a cDNA, or a restriction fragment.In another embodiment, an isolated nucleic acid is preferably excisedfrom the chromosome in which it may be found, and more preferably is nolonger joined to non-regulatory, non-coding regions, or to other genes,located upstream or downstream of the gene contained by the isolatednucleic acid molecule when found in the chromosome. In yet anotherembodiment, the isolated nucleic acid lacks one or more introns.Isolated nucleic acids include sequences inserted into plasmids,cosmids, artificial chromosomes, and the like. Thus, in a specificembodiment, a recombinant nucleic acid is an isolated nucleic acid. Anisolated protein may be associated with other proteins or nucleic acids,or both, with which it associates in the cell, or with cellularmembranes if it is a membrane-associated protein. An isolated organelle,cell, or tissue is removed from the anatomical site in which it is foundin an organism. An isolated material may be, but need not be, purified.

The terms “about” and “approximately” shall generally mean an acceptabledegree of error for the quantity measured given the nature or precisionof the measurements. Typical, exemplary degrees of error are within 20percent (%), preferably within 10%, and more preferably within 5% of agiven value or range of values. Alternatively, and particularly inbiological systems, the terms “about” and “approximately” may meanvalues that are within an order of magnitude, preferably within 10- or5-fold, and more preferably within 2-fold of a given value. Numericalquantities given herein are approximate unless stated otherwise, meaningthat the term “about” or “approximately” can be inferred when notexpressly stated.

Method of Determining Treatment Options

To easily determine whether SPC therapy will be a viable treatment forpatients, for example, Fabry, Pompe or Gaucher patients, and includingfemale carriers of X-linked lysosomal storage disorders such as Fabrydisease, a simple, non-invasive SPC rescue assay of protein activity ina cell line expressing a mutant form of the protein was developed.

In Vitro Assay

In one embodiment, the diagnostic method of the present inventioninvolves transforming a cell line with a nucleic acid vector whichencodes a mutant lysosomal enzyme, for example, α-Gal A, GAA or Gba. Thecell line is then treated with or without an SPC, e.g., DGJ, DNJ or IFG,for a sufficient time period to demonstrate enhancement (i.e., increase)of α-Gal A, GAA or Gba activity. The transformed cells are then lysed,and the lysate is used in an assay to determine enzyme activity. Asufficient increase in α-Gal A, GAA or Gba activity in the lysates fromcells treated with the SPC over the activity in the lysates fromuntreated cells indicates that a patient who expresses α-Gal A, GAA orGba with the same mutation as the cell line will likely respond to SPCtherapy (i.e., the patient will be a “responder”).

Transient Transfection of a Cell Line and Expression of a MutantLysosmal Enzyme

In one embodiment, to identify SPC-responsive mutations, all knownlysosomal enzyme (e.g., α-Gal A, GAA or Gba) mutations, for example,missense mutations and in-frame small deletions and insertions, can begenerated according to techniques known in the art, for example, bysite-directed mutagenesis. Mutant enzyme constructs can then betransiently expressed in a cell line, for example, mammalian COS-7,HEK-293 or GripTite 293 MSR (Invitrogen Corp., Carlsbad, Calif., U.S.A.)cells. Transformed cells can then be incubated with increasingconcentrations of SPC and enzymatic activity can be measured in celllysates.

Mutagenesis:

Nucleic acid vectors encoding a mutant protein (e.g. mutant α-Gal A, GAAor Gba) can be generated by conventional molecular biology,microbiology, and recombinant DNA techniques within the skill of theart. Such techniques are explained fully in the literature. (See, e.g.,Sambrook, Fritsch & Maniatis, 2001, Molecular Cloning: A LaboratoryManual, Third Edition, Cold Spring Harbor Laboratory Press, Cold SpringHarbor, N.Y.; Glover, ed., 1985, DNA Cloning: A Practical Approach,Volumes I and II, Second Edition; Gait, M. J., ed., 1984,Oligonucleotide Synthesis: A practical approach; Hames, B. D. & Higgins,S. J., eds., 1985, Nucleic Acid Hybridization; Hames, B. D. & Higgins,S. J., eds., 1984, Transcription And Translation; Freshney, R. I., 2000,Culture of Animal Cells: A Manual of Basic Technique; Woodward, J.,1986, Immobilized Cells And Enzymes: A practical approach, IRL Press;Perbal, B. E., 1984, A Practical Guide To Molecular Cloning). Forexample, a single α-Gal A, GAA or Gba mutation can be introduced into anucleic acid encoding a wild type α-Gal A, GAA or Gba gene through sitedirected mutagenesis of a nucleic acid encoding the wild type enzyme.

Transient Transfection and Expression:

The coding sequences of the gene to be delivered, for example, a mutantα-Gal A, GAA or Gba, are operably linked to expression controlsequences, e.g., a promoter that directs expression of the gene. As usedherein, the phrase “operatively linked” refers to the functionalrelationship of a polynucleotide/gene with regulatory and effectorsequences of nucleotides, such as promoters, enhancers, transcriptionaland translational stop sites, and other signal sequences. For example,operative linkage of a nucleic acid to a promoter refers to the physicaland functional relationship between the polynucleotide and the promotersuch that transcription of DNA is initiated from the promoter by an RNApolymerase that specifically recognizes and binds to the promoter. Thepromoter directs the transcription of RNA from the polynucleotide.Expression of a mutant protein (e.g. mutant α-Gal A, GAA or Gba) may becontrolled by any promoter/enhancer element known in the art, but theseregulatory elements must be functional in the host selected forexpression.

In one specific embodiment, a vector is used in which the codingsequences and any other desired sequences are flanked by regions thatpromote homologous recombination at a desired site in the genome, thusproviding for expression of the construct from a nucleic acid moleculethat has integrated into the genome (See Koller and Smithies, 1989,Proc. Natl. Acad. Sci. USA, 86:8932-8935: Zijlstra et al., 1989, Nature342:435-438; U.S. Pat. No. 6,244,113 to Zarling et al.; and U.S. Pat.No. 6,200,812 to Pati et al.).

The term “host cell” means any cell of any organism that is selected,modified, transformed, grown, or used or manipulated in any way, for theproduction of a substance by the cell, for example the expression by thecell of a gene, a DNA or RNA sequence, a protein or an enzyme. In oneembodiment, a host cells that is transfected with a vector encoding amutant α-Gal A, GAA or Gba can be used for screening a candidate SPC,for example, DGJ, DNJ or IFG, to determine if the candidate SPC is aneffective compound for increasing the activity of the mutant α-Gal A,GAA or Gba expressed by the host cell.

The term “expression system” means a host cell and compatible vectorunder suitable conditions, e.g., for the expression of a protein codedfor by foreign DNA carried by the vector and introduced to the hostcell. Expression systems include mammalian host cells and vectors.Suitable cells include PC12 cells, CHO cells, HeLa cells, GripTite 293MSR cells (Invitrogen Corp., Carlsbad, Calif., U.S.A.), HEK-293 (alsoknown as 293 cells) and 293T cells (derived from human embryonic kidneycells), COS cells (e.g. COS-7 cells), mouse primary myoblasts, NIH 3T3cells.

Suitable vectors include viruses, such as adenoviruses, adeno-associatedvirus (AAV), vaccinia, herpesviruses, baculoviruses and retroviruses,parvovirus, lentivirus, bacteriophages, cosmids, plasmids, fungalvectors, naked DNA, DNA lipid complexes, and other recombinationvehicles typically used in the art which have been described forexpression in a variety of eukaryotic and prokaryotic hosts, and may beused for gene therapy as well as for simple protein expression.

In one non-limiting example, transient transfection can be carried outin GripTite 293 MSR cells (Invitrogen Corp., Carlsbad, Calif., U.S.A.)using the reagent Fugene HD (Roche). The cells can be seeded in asuitable assay container, such as a 96-well plate (Costar) at a densityof, for example, 7.5-10 k cells/well, and incubated under suitableconditions, such as, for example, 37° C., 5% CO₂ for 24 hours beforetransfection. After transfection with expression constructs containing aspecific α-Gal A mutant, cells can be incubated again in, for example,37° C., 5% CO₂ for one hour before adding DGJ at 50 nM to 1 mM. Cellscan then be incubated for 4-5 days before lysis and assay.

Enzyme Activity/Enhancement Assay:

Typically, following incubation with an SPC (e.g. DGJ, DNJ or IFG), hostcells are lysed by the addition of lysis buffer (or deionized water) andphysical disruption (pipetting, vortexing and/or agitation, and/orsonication) at room temperature or on ice, followed by pooling of thelysates on ice, then splitting the pooled lysate into small aliquots andfreezing.

The lysates can be thawed immediately prior to the assay and should besuspended by use of a vortex mixer and sonicated prior to addition toappropriate wells e.g., in a microplate. In the context of Fabrydisease, N-acetylgalactosamine (GalNAc) is then added to each well (toinhibit α-galactosidase B), followed by a short incubation.4-methylumbelliferyl-α-D-galactopyranoside (4-MU Gal), or otherappropriate labeled DGJ substrate, is then added and the plate is gentlymixed for a brief period of time, covered, and incubated at 37° C. for asufficient time for substrate hydrolysis, usually about 1 hour. To stopthe reaction, NaOH-glycine buffer, pH 10.7, is added to each well andthe plate is read on a fluorescent plate reader (e.g. Wallac 1420Victor3™ or similar instrument). Excitation and emission wavelengthswere customarily set at 355 nm and 460 nm, respectively. One unit ofenzyme activity is defined as the amount of enzyme that catalyzes thehydrolysis of 1 nmole of 4-methylumbelliferone per hour. For eachpatient sample at least three normal samples may be tested concurrently.

Various modifications of this assay will be readily ascertainable to oneof ordinary skill in the art. Examples of artificial substrates that canbe used to detect α-Gal A activity include but are not limited top-nitrophenyl-α-D-galactopyranoside and 4-MU GAL. Obviously, onlysubstrates that can be cleaved by human α-Gal A are suitable for use. Itis noted that while use of a fluorogenic substrate is preferred, othermethods of determining enzymatic activity are contemplated for use inthe method, including using chromogenic substrates orimmunoquantification techniques.

In one specific example, following incubation with an SPC, for example,DGJ, the host cells can be washed two times with PBS then incubated in200 μl fresh media at 37° C., 5% CO₂ for two hours followed by 2additional PBS washes. After, cells can be lysed in 60 μL Lysis Buffer(27 mM sodium citrate/46 mM sodium phosphate dibasic, 0.5% Triton X-100,pH 4.6). Ten μL lysate can then be added to 50 μL assay buffer (LysisBuffer without Triton X-100, but containing 6 mM4-MU-α-D-galactopyranoside (4-MUG) and 117 mM N-acetyl-D-galactosamine(GalNac)), and incubated at 37° C. for 1 hr. Seventy μL Stop Solution(0.4 M glycine, pH 10.8) can then be added and fluorescence read on aVictor plate reader (Perkin Elmer) at 355 nm excitation and 460 nmemission. Raw fluorescence counts can be background subtracted asdefined by counts from substrate solution only. A MicroBCA Protein AssayKit (Pierce) was used according to manufacturer's instructions todetermine protein concentration from 40 μL of cell lysate. A4-methylumbelliferone (4-MU) standard curve ranging from 30 μM to 1.3 nMwas run in parallel for calculation of absolute α-Gal A activityexpressed as nmoles/mg protein/hr or further normalized to % ofuntreated wild type enzyme activity.

Treatment Reference Table

In another embodiment, the methods described supra can be used togenerate a “treatment reference table” or “treatment therapy table,”wherein the treatment reference table comprises a list of proteinmutations, and further wherein the table indicates the responsiveness ofeach mutation to an SPC, such as DGJ, DNJ or IFG. The treatmentreference table can then be used to determine if a particular SPC, forexample, DGJ. DNJ or IFG, would be an effective SPC for treating apatient with a particular α-Gal A, GAA or Gba mutation, respectively.

As used herein “treatment therapy table” or “treatment reference table”refers to any written record that conveys whether a particular mutationis responsive to SPC therapy, and is not necessarily limited to writtenrecords presented in tabular form.

In one embodiment, the treatment reference table can be used by atreating physician or clinical professional to select an SPC fortreating a patient, for example, a Fabry, Pompe or Gaucher patient whoexpresses a specific mutant α-Gal A, GAA or Gba, respectively, whereinthe SPC is selected because the treatment reference table identifies theSPC as a compound that can increase the activity of the patient's mutantα-Gal A, GAA or Gba when the mutant α-Gal A, GAA or Gba is expressed ina host cell.

Treatable Disorders

While the present application has been discussed largely in the contextof Fabry, Pompe and Gaucher diseases, and the SPCs DGJ, DNJ and IFG,respectively, it should be understood that it is applicable to any SPCand disease. In one non-limiting embodiment, a treatment reference tablecan be generated for any candidate SPC and any lysosomal storagedisorder, or any disorder involving protein misfolding. These diseasesinclude other lysosomal storage disorders, for example, Cystic Fibrosis(CFTR) (respiratory or sweat gland epithelial cells), familialhypercholesterolemia (LDL receptor; LPL-adipocytes or vascularendothelial cells), cancer (p53; PTEN-tumor cells), Alzheimer's disease(α-secretase), Parkinson's disease (glucocerebrosidase), obesity (MC4R),and amyloidoses (transthyretin) among others.

Eligibility Determination Criteria

The criteria for determining eligibility for SPC therapy depends on thetype of mutant GLA, GAA or Gba a patient expresses. In one embodiment,patients with Fabry, Pompe, or Gauchcr disease could be categorized aseligible for SPC therapy if α-Gal A, GAA or Gba activity, respectively,in a host cell expressing the same mutation as the patient, in thepresence of an SPC such as DGJ, DNJ or IFG, is at least about 1.5- to20-fold (2% to 100%) activity of a host cell expressing a wild typeα-Gal A, GAA or Gba.

This discovery provides a method for improving the diagnosis of andfacilitating clinical treatment decisions for Fabry, Pompe and Gaucherdiseases in particular, and lysosomal storage disease in general.Moreover, this method can be extended to a wide range of geneticallydefined diseases in appropriate cell types. This class of diseaseincludes the other lysosomal storage disorders, Cystic Fibrosis (CFTR)(respiratory or sweat gland epithelial cells), familialhypercholesterolemia (LDL receptor; LPL-adipocytcs or vascularendothelial cells), cancer (p53; PTEN-tumor cells), Alzheimer's disease(α-secretase), Parkinson's disease (glucocerebrosidase), obesity (MC4R),and amyloidoses (transthyretin) among others.

Kits

The present invention also provides for a commercial diagnostic test kitin order to make therapeutic treatment decisions. The kit provides allmaterials discussed above and more particularly in the Examples below,for preparing and running each assay in one convenient package,optionally including instructions and an analytic guide.

As one non-limiting example, a kit for evaluating α-Gal A activity maycontain, at a minimum:

-   -   a. a panel of host cells, each expressing a mutant α-Gal A, or        alternatively, a host cell, a vector encoding a mutant α-Gal A,        and a means of transfecting the host cell such that the host        cell expresses the mutant α-Gal A;    -   b. a specific pharmacological chaperone;    -   c. a chromogenic or fluorogenic substrate for the enzyme assay        (including an appropriate standard); and    -   d. GalNAc.        The kit may also contain instructions for optimally performing        the protein enhancement assay. In another embodiment, the kit        will contain the appropriate tubes, buffers (e.g., lysis        buffer), and microplates.

In one embodiment, the SPC is supplied in dry form, and will bere-constituted prior to addition.

Patients who express a mutant α-Gal A, GAA or Gba that previously testedpositive for enzyme enhancement with a candidate SPC in assays of thepresent invention can then be treated with that candidate SPC agent,whereas patients who express a mutant α-Gal A, GAA or Gba that does notdisplay enzyme enhancement with a candidate SPC can avoid treatmentwhich will save money and prevent the emotional toll of not respondingto a treatment modality.

EXAMPLES

The present invention is further described by means of the examples,presented below. The use of such examples is illustrative only and in noway limits the scope and meaning of the invention or of any exemplifiedterm. Likewise, the invention is not limited to any particular preferredembodiments described herein. Indeed, many modifications and variationsof the invention will be apparent to those skilled in the art uponreading this specification. The invention is therefore to be limitedonly by the terms of the appended claims along with the full scope ofequivalents to which the claims are entitled.

Example 1: Identification of Fabry Disease-Causing Mutations that areResponsive to the Pharmacological Chaperone DGJ

The present Example provides the in vitro diagnostic assay to determinea Fabry patient's responsiveness to a specific pharmacologicalchaperone.

INTRODUCTION

Fabry disease is a lysosomal storage disorder caused by mutations in thegene that encodes α-galactosidase A (α-GAL A). Over 600 Fabry mutationshave been reported, and about 60% are missense. The iminosugar DGJ iscurrently being studied in Phase 2 clinical trials as a pharmacologicalchaperone for the treatment of Fabry disease. Previously, it has beenshown that DGJ mediates selective and dose-dependent increases in α-GalA levels in many Fabry patient-derived lymphoid cell lines. To identifyadditional DGJ-responsive mutations, GripTite 293 MSR, (InvitrogenCorp., Carlsbad, Calif., U.S.A.) cells were transiently transfected withexpression vectors containing all known α-Gal A missense mutations andseveral in-frame small deletions and insertions generated bysite-directed mutagenesis. Mutant α-Gal A constructs were transientlyexpressed in HEK-293 cells. Cells were incubated with increasingconcentrations of DGJ and α-Gal A activity was measured in cell lysates.Assay validation has been carried out on more than 35 missense mutationsand the results obtained in HEK-293 cells were similar to those obtainedfrom both Fabry patient-derived lymphoid cells and primary T-cellcultures (see U.S. Ser. No. 11/749,512), as well as to the α-Gal Aenzyme responses observed in the white blood cells of Fabry patientsafter oral administration of DGJ in Phase 2 clinical trials.

Methods and Materials

Mutagenesis:

All mutations were generated by site-directed mutagenesis followingstandard molecular biology protocols. To generate point mutations,site-directed mutagenesis was used on the expression vector pcDNA3.1(Invitrogen) containing human α-GAL A cDNA in-frame. Specific primerpairs were designed containing the desired mutation (FIG. 6). Themutagenesis was performed through the polymerase chain reaction usingPfuUltra high-fidelity DNA polymerase (Stratagene) in a thermocycler.Each reaction mixture contained a total volume of 50 μl with thefollowing: 41.6 μl dH₂O, 5.0 μl 10× PfuUltra HF reaction buffer, 0.5 μl.Forward-5′-primer (50 uM), 0.5 μl Reverse-3′-primer, 1.0 μl dNTP mix(containing 25 mM each dA, dT, dC, dG), 0.9 μl human GLA in pcDNA3 (2ng/μl DNA), 0.5 pt PfuUltra HD DNA polymerase. Thermocycler parameterused was the following: i) 94° C. for 30 seconds, ii) 94° C. for 30seconds, 55-60° C. for 30 seconds, 68° C. for 6 minutes, iii) Repeat(ii) 16 times. Afterwards, 0.5 μl Dpn I (New England Biolabs) was addedto each reaction and incubated at 37° C. for 2 hours. A volume of 7.5 μlfor each mutagenesis reaction was used to transform DH5α cells (NewEngland Biolabs). Cells were then plated on LB-agar plates with 75 ug/mlampicillin, and incubated at 37° C. overnight. Bacterial colonies werepicked, grown in liquid LB with ampicillin overnight, shaking, at 37°C., and plasmid DNA extracted using QuickLyse Miniprep Kit (Qiagen).Mutants were confirmed by sequencing the full-length human GLA gene. Forsome of the mutants, human GLA cDNA was contained in the vector plasmidpCXN. Mutagenesis was performed in this vector with the NEB Fusion DNApolymerase. After confirming the mutation through sequencing, theplasmid was digested with EcoRI and subcloned into expression vectorpcDNA3.1. Correct orientation was confirmed by digestion with Xho I.

Transient Transfection and Expression:

Transient transfection was carried out in GripTite 293 MSR cells(Invitrogen Corp., Carlsbad, Calif., U.S.A.) using the reagent Fugene HD(Roche). Briefly, cells were seeded in 96-well plates (Costar) at adensity of 7.5-10 k cells/well and incubated at 37° C., 5% CO₂ for 24hours before transfection. Cells were transfected with 0.1 μg DNA and0.35 μL of Fugene HD reagent per well (DNA:Reagent ratio of 2:7). Aftertransfection with expression constructs containing the specific α-Gal Amutants, cells were incubated again in 37° C., 5% CO₂ for one hourbefore adding DGJ at 20 nM to 1 mM. Cells were then incubated for 4-5days before lysis and assay.

α-GAL A Activity Measurement:

Cells were washed two times with PBS then incubated in 200 μl freshmedia at 37° C., 5% CO₂ for two hours followed by 2 additional PBSwashes. After, cells were lysed in 60 μL Lysis Buffer (27 mM sodiumcitrate/46 mM sodium phosphate dibasic, 0.5% Triton X-100, pH 4.6). TenμL lysate were added to 50 μL assay buffer (Lysis Buffer without TritonX-100, but containing 6 mM 4-MU-α-D-galactopyranoside (4-MUG) and 117 mMN-acetyl-D-galactosamine (GalNac)), and incubated at 37° C. for 1 hr.Seventy μL Stop Solution (0.4 M glycine, pH 10.8) were then added andfluorescence read on a Victor plate reader (Perkin Elmer) at 355 nmexcitation and 460 nm emission. Raw fluorescence counts were backgroundsubtracted as defined by counts from substrate solution only. A MicroBCAProtein Assay Kit (Pierce) was used according to manufacturer'sinstructions to determine protein concentration from 40 μL of celllysate. A 4-methylumbelliferone (4-MU) standard curve ranging from 30 μMto 1.3 nM was run in parallel for calculation of absolute α-Gal Aactivity expressed as nmoles/mg protein/hr or further normalized to % ofuntreated wild type enzyme activity.

Transient transfection and α-Gal A activity measurements were performedin quadruplicates and repeated at least 3 times for each mutation tocalculate the average α-Gal A activity at each DGJ concentration.Significant response to DGJ was determined by a two-tailed, pairedStudent's T-test (p<0.05).

Results

All listed Fabry mutations were generated by site-directed mutagenesis(FIG. 1). Mutations identified in italicized text were not tested, whilethose identified in plain text were α-Gal A mutants that were responsiveto DGJ treatment in the transient transfection assay, and thoseidentified in bold and underscored text were not responsive to DGJtreatment in the transient transfection assay. The magnitude of increasein α-Gal A levels after DGJ treatment and EC50 values are listed forevery tested mutation that responded to DGJ treatment (FIG. 2).

α-Gal A activity (expressed as nmol/mg protein/hr of 4-MU released) wasmeasured in lysates prepared from transfected GripTite 293 cellsincubated with increasing concentrations of DGJ. A typicalconcentration-dependent response is shown for L300P and a typicalnegative response to DGJ is shown for R227Q. Wild type exhibits highbaseline activity and does not respond to DGJ in this assay (FIG. 3).

α-Gal A levels were measured in three different assays, reported aspercentage of wild type, are compared for each mutation by plotting sideby side. The three different assays examined α-Gal A levels in T-cellsand lymphoblasts isolated from Fabry patients (for example, see U.S.Ser. No. 11/749,512), as well as in white blood cell (WBC) from DGJPhase 2 studies

Blank bars indicate basal level (without DGJ treatment) and filled barsindicate the elevated level after DGJ treatment (FIG. 4).

Tested Fabry mutations were illustrated on the α-Gal A secondarystructure (FIG. 5). No significant correlation between response andlocation on the protein sequence of a mutation was observed, suggestingthat responsive as well as non-responsive mutations are distributedwidely across the entire protein. Text color indicates DGJ response:green=response; red=no response; brown indicates that of the multiplemutations on that same site some responded to DGJ treatment, whileothers did not.

CONCLUSION

These described results are comparable to those obtained from Fabrypatient-derived lymphoid or T cells, as well as to the α-Gal A enzymeresponses observed in the white blood cells of Fabry patients after oraladministration of DGJ in Phase 2 clinical trials.

Thus, the GripTite 293 MSR transient transfection assay is a reliablemethod for identifying DGJ-responsive mutations and characterizing themagnitude and potency of this response.

Among the responsive mutations identified, the increases in α-Gal Alevels by DGJ treatment ranged from 1.3- to 40-fold (2% to 100% wildtype), with EC₅₀ values between 200 nM and >100 mM.

DGJ-responsive and non-responsive mutant forms did not appear to belocated to particular regions or domains on the α-Gal A proteinstructure.

Example 2: Ex Vivo Method for Evaluating Effects of an SPC onGlucocerebrosidase Activity—Prophetic Example

Gaucher disease (GD) is caused by a deficiency of lysosomalglucocerebrosidase (GCase). Deficient GCase activity leads to anaccumulation of glucosylceramide (GlcCer) and the development ofsymptoms such as anemia, thrombocytopenia, hepatosplenomegaly, bonenecrosis, infarcts and osteoporosis, and in some cases, neuropathicdisease. The specific pharmacological chaperone isofagomine tartrate(IFG) selectively binds and stabilizes mutant (N370S/N370S) GCase in theER and increases its trafficking to the lysosome.

To evaluate the effects of IFG on different GCase variants, an ex vivodiagnostic assay will be prepared using Cos7 cells in order to ascertainIFG-responsive mutations.

Using the techniques described in Examples 1 and 4, COS-7 cell lineswill be prepared that express missense mutations and several in-framesmall deletions and insertions by site-directed mutagenesis. Assays willbe prepared for all of the mutations listed in the x-axis of FIG. 8.IFG-activity response will be ascertained for each assay according tomethods known in the art (see, e.g., U.S. Pat. No. 6,916,829, which ishereby incorporated by reference).

To determine the correlation of the IFG-response measured in the COS-7cells to patient-derived cells, IFG-activity response was also measuredin Patient-Derived Macrophages and Lymphoblasts. Macrophages weresuccessfully derived from 46 of 63 patients and incubation with IFG (3,10, 30 or 100 μM) for 5 days increased GCase levels in macrophages from42 of 46 patients (mean=2.3-fold; range: 1.1- to 6.5-fold). Residualactivity levels and response to IFG was more consistent for the samegenotypes when measured in lymphoblasts compared to macrophages,potentially due to the variability in macrophage viability betweendifferent patients. The results are shown in FIG. 8.

The response to IFG for the patient-derived cells will be compared tothe results obtained in the Cos7 cell line.

Example 3: In Vivo Effect of an SPC on α-GAL A Activity in Skin, Heart,Kidney and Plasma

To determine if increased mutant α-Gal A levels translate to increasedα-Gal A activity in situ, the effect of DGJ administration on tissueGL-3 levels was investigated in vivo in hR301Q α-Gal A Tg/KO mice.

Eight-week old male hR301Q α-Gal A Tg/KO mice were treated for 4 weekswith 300 mg/kg DGJ in drinking water either daily or less frequently (4days ON/3 days OFF). After dosing, lysates were prepared from skin,heart, kidney, and plasma by homogenizing ˜50 mg tissue in Lysis Buffer(see above). 20 μL lysate were mixed with 50 μL of substrate (asdetailed above). Reaction mixtures were incubated at 37° C. for 1 hr.After, 70 μL Stop Solution were added and fluorescence was read on aVictor plate reader as described above. Enzyme activity in the lysateswas background subtracted, and normalized for protein concentration. A4-MU standard curve was run for conversion of fluorescence data toabsolute α-Gal A activity expressed as nmol/mg protein/hr.

Tissue samples were washed free of blood, weighed and homogenized with asolvent system in a FastPrep® system. Homogenate was then extractedusing Solid Phase Extraction on a C18 cartridge. The eluent wasevaporated and reconstituted prior to injection onto a LC-MS/MS system.Twelve GL-3 isoforms were measured using positive ESI-MS/MS. LCseparation was achieved on 00839a Zorbax C18 column.

Significant decreases in GL-3 levels were seen with daily and lessfrequent DGJ dosing in skin, heart, kidney, and plasma (FIG. 9). A trendof greater reduction in GL-3 levels was seen in multiple tissues andplasma with less frequent DGJ dosing. Collectively, these resultsindicate that DGJ merits further evaluation for the treatment ofpatients with Fabry disease.

Example 4: Identification of Pompe Disease-Causing Mutations That AreResponsive to the Pharmacological Chaperone DNJ

Pompe disease is caused by deficient acid alpha glucosidase (GAA)activity which impairs lysosomal glycogen metabolism. The enzymedeficiency leads to lysosomal glycogen accumulation and results inprogressive skeletal muscle weakness, reduced cardiac function,respiratory insufficiency, and CNS impairment at late stages of disease.Genetic mutations in the GAA gene result in either lower expression orproduce mutant forms of the enzyme with altered stability, and/orbiological activity ultimately leading to disease. Pharmacologicalchaperones represent a promising new therapeutic approach for thetreatment of genetic diseases.

To evaluate the effects of DNJ on different GAA variants, an in vitrodiagnostic assay was prepared using COS-7 and HEK-293 cells in order toascertain DNJ-responsive mutations (FIGS. 10, 12 and 14)

A site-directed mutagenesis approach was employed to introduce specificmutations into the complementary DNA (cDNA) encoding wild-type humanacid α-glucosidase (GAA). The initial wild-type GAA DNA construct wasgenerated by subcloning the GAA coding region from cDNA clone 5739991(Invitrogen) into the pcDNA6N5-HisA mammalian expression vector(Initrogen). The resultant DNA construct (designated as wild-type GAAcDNA) was used as the DNA template for subsequent mutagenesis. Thesemissense, small insertion or deletion mutations are cited in the Erasmusdatabase and known to be associated with type 2 glycogen storagedisorder (GSD II), also known as Pompe disease. Briefly, wild-type GAAcDNA was PCR-amplified using mutagenic primers to obtain plasmid DNAwith the desired mutation These mutations were confirmed by DNAsequencing prior to protein expression in cells.

COS-7 cells (derived from green monkey embryonic kidney cells) wereaseptically seeded in 12-well tissue culture plates at a cell density of˜1.4×10⁵ cells per well in 3 ml of Dulbecco's Modified Essential Medium(DMEM) containing 10% (v/v) fetal bovine serum and grown overnight at37° C. in a humidified 5% CO₂ atmosphere. On the following day, thecells (typically 60-80% confluent) were transfected with 0.75 μg of theindividual DNA construct via a lipid transfection reagent such as FUGENEHD (Roche) according the manufacturer's instructions. Two wells weretransfected with each DNA construct such that one well was incubatedwith DNJ (typically 0 μM, 20 μM, 50 μM or 100 μM) while an equivalentvolume of PBS was added to the other well. Two additional wells weretransfected with the empty vector (no GAA cDNA) and incubated with orwithout DNJ to serve as the background control for endogenous monkey GAAexpression. Similarly, 2 additional wells were transfected with thewild-type human GAA cDNA and incubated with or without DNJ to serve asthe positive control. All samples were incubated for ˜48 hrs at 37° C.in a humidified 5% CO₂ atmosphere.

After the 48-hour incubation period, the spent media was removed and thecells were washed with PBS and then incubated with fresh 1-2 ml DMEMmedium for 3 hours at 37° C. in a humidified 5% CO₂ atmosphere. Themedium was subsequently removed and cells were immediately washed withPBS and lysed with 200 μl of Lysis Buffer (25 mM Bis-Tris (pH 6.5), 150mM NaCl, 1% (v/v) Triton X-100) containing a cocktail of proteaseinhibitors. The cell culture plate were then gently swirled on arotating orbital shaker apparatus for 10 min at room temperature forcomplete cell lysis. The resultant cell lysates were transferred toclean 1.5 ml microcentrifuge tubes and spun at 20,000×g for 10 mM topellet cellular debris. Approximately 175 μl of each supernatant samplewas then transferred to a 1.5 ml fresh microcentrifuge tube. This celllysate was used for all subsequent assays including GAA enzyme activity,total protein concentration determination, and Western blotting.

Residual GAA enzyme activity was determined for eachtransiently-expressed GAA using a fluorogenic4-methylumbeliferyl-α-glucopyranoside (4-MU-α-glucose) substrate(Sigma). Briefly, 10 μl of each cell lysate was assayed (in triplicate)in a 100 μl reaction in 96-well clear bottom black plates using 3 mM4-MU-α-glucose and 50 mM KOAc (pH 4.0). The transiently-expressedwild-type GAA sample was diluted 20-fold with Lysis Buffer to ensurethat the enzymatic reaction is maintained within the linear range of theinstrument. The enzyme reactions were performed at 37° C. for 1 hour andterminated by the addition of 50 μl of 500 mM Na₂CO₃ (pH 10.5). Theassay was then read in a fluorescence plate reader (using 355 nmexcitation/460 nm emission) to quantitate the amount of GAA-dependent4-MU fluorescence liberated. The GAA enzyme activity was thenextrapolated from a free 4-MU standard curve after subtracting thebackground fluorescence (i.e., empty vector control).

Twenty five microliters of each cell lysate was used in a parallel assayto determine the total cellular protein concentration using thebicinchoninic acid (BCA) protein assay (Pierce) according to themanufacturer's protocol. The total cellular protein concentration wasextrapolated from a bovine serum albumin (BSA) standard curve.

The GAA enzyme activity for each sample was normalized to the totalcellular protein concentration and expressed as the nmoles of 4-MUreleased/mg total protein/hr to define the GAA specific activity. Theresultant GAA specific activity after DNJ treatment was compared to GAAenzyme activity of the corresponding untreated sample to determinewhether a specific GAA mutant responds to DNJ.

For a single HEK-293 cell line transfected with the GAA mutation, P545L,the DNJ EC₅₀ was also determined (FIG. 14).

To determine the correlation of the DNJ-response measured in the COS-7cells to patient-derived cells, DNJ-activity response was also measuredex vivo in Patient-Derived Macrophages and Lymphoblasts.

Fibroblast and lymphocyte cell lines derived from Pompe patients werealso generated as previously described (see U.S. Ser. No. 11/749,512).Fibroblast cell lines were derived from patients homozygous for theP545L or R854X GAA mutations (FIG. 13). Lymphocyte cell lines werederived from patients heterozygous for the (IVS1AS, T>G, −13) GAAsplicing defect and GAA frameshift mutation (FIG. 15).

GAA activity was measured in the lymphocyte cell lines followingincubation in 0 μM, 30 μM, 100 μM, or 300 μM DNJ (FIG. 15). GAA activitywas also measured in the fibroblast cell lines following DNJ incubation(FIG. 13).

In this study, the pharmacological chaperone 1-deoxynojirimycin-HC (DNJ)is shown to bind mutant GAA and increase its activity. In Pompepatient-derived fibroblasts (FIG. 13) and lymphocytes (FIG. 15), as wellas in transiently transfected COS-7 (FIGS. 10 and 12) or HEK-293 (FIG.14) cells expressing certain GAA missense mutations, DNJ significantlyincreases GAA levels.

DNJ increased GAA activity for 26 mutations (FIG. 10) out of 131 mutantstested (data not shown). In addition to increasing the activity of thesemutant GAA's, DNJ also promoted processing of GAA to the 95/76/70 kDaforms.

Furthermore, dose-dependent increases in GAA activity was observed inpatient-derived lymphocytes containing the common IVS1AS, T>G, −13splicing defect in one allele and a frameshift mutation in the secondallele (FIG. 15).

The present invention is not to be limited in scope by the specificembodiments described herein. Indeed, various modifications of theinvention in addition to those described herein will become apparent tothose skilled in the art from the foregoing description and theaccompanying figures. Such modifications are intended to fall within thescope of the appended claims.

Patents, patent applications, publications, product descriptions,GenBank Accession Numbers, and protocols are cited throughout thisapplication, the disclosures of which are incorporated herein byreference in their entireties for all purpose.

The invention claimed is:
 1. A method of treating a patient diagnosedwith Fabry disease which comprises administering to the patient atherapeutically effective dose of 1-deoxygalactonorjirimycin or a saltthereof, wherein the patient is identified as having a mutantα-galactosidase A, relative to a human α-galactosidase A encoded by anucleic acid sequence set forth in SEQ ID NO:2, said mutation selectedfrom the group consisting of the α-galactosidase A mutations D33Y, L36F,A37V, M42L, M42T, M42R, M51I, L54P, D55V, D55V/Q57L, C56F, C56Y, P60L,E66K, E66G, G85D, G85M, A97P, R118C, A135V, Y152C, A156T, W162G, F169S,G183A, Y184C, M187V, M187T, L191Q, V199M, P205S, P205L, N215D, Y216D,Y216C, S238N, I239T, L243W, S247C, Q250P, I253T, 254del1, A257P, V269A,P293T, R301G, A309P, D313G, Q321L, G325S, V339E, E358G, I359T, G360S,G360D, P362L, 401ins/T401S, P409T, T410A, T410I and G411D.
 2. The methodof claim 1, wherein the mutation is selected from the group consistingof: D33Y, L36F, A37V, M42L and M42T.
 3. The method of claim 1, whereinthe mutation is selected from the group consisting of: M42R, M51I, L54P,D55V and D55V/Q57L.
 4. The method of claim 1, wherein the mutation isselected from the group consisting of: C56F, C56Y, P60L, E66K and E66G.5. The method of claim 1, wherein the mutation is selected from thegroup consisting of: G85D, G85M, A97P, R118C and A135V.
 6. The method ofclaim 1, wherein the mutation is selected from the group consisting of:Y152C, A156T, W162G, F169S and G183A.
 7. The method of claim 1, whereinthe mutation is selected from the group consisting of: Y184C, M187V,M187T, L191Q and V199M.
 8. The method of claim 1, wherein the mutationis selected from the group consisting of: P205S, P205L, N215D, Y216D andY216C.
 9. The method of claim 1, wherein the mutation is selected fromthe group consisting of: S238N, I239T, L243W, S247C and Q250P.
 10. Themethod of claim 1, wherein the mutation is selected from the groupconsisting of: I253T, 254del1, A257P, V269A and P293T.
 11. The method ofclaim 1, wherein the mutation is selected from the group consisting of:R301G, A309P, D313G and Q321L.
 12. The method of claim 1, wherein themutation is selected from the group consisting of: G325S, V339E, E358Gand I359T.
 13. The method of claim 1, wherein the mutation is selectedfrom the group consisting of: G360S, G360D, P362L and 401ins/T401S. 14.The method of claim 1, wherein the mutation is selected from the groupconsisting of: P409T, T410A, T410I and G411D.
 15. The method of claim 1,wherein the patient is male.
 16. The method of claim 1, wherein thepatient is female.
 17. The method of claim 1, wherein the1-deoxygalactonojirimycin is in a pharmaceutically acceptable salt form.18. The method of claim 17, wherein the pharmaceutically acceptable saltform is 1-deoxygalactonojirimycin hydrochloride.